In these experiments glycinergic fibers were photactivated while the firing rate of individual IL neurons was recorded. Some of the IL cells had very low baseline activity. In order to increase the firing rate of the IL neurons and to detect the effect of the glycinergic fiber activation a small tail pinch was applied. The firing rate of the recorded IL cells decreased during the glycinergic fiber activation.
Loading AP and stimuli times from stimulus and from baseline data to IL_stim_firing and to IL_baseline_firing tables:
IL_stim_firing <- CreateRecTibble(AP_times = read_csv(file.path("data",
"IL_MFR", "stimulus", "AP_times.csv")),
stim_times = read_csv(file.path("data",
"IL_MFR", "stimulus", "stim_times.csv")))
IL_stim_firing %>% head()
IL_baseline_firing <- CreateRecTibble(
AP_times = read_csv(file.path("data", "IL_MFR","baseline", "AP_times.csv")),
stim_times = read_csv(file.path("data", "IL_MFR","baseline", "stim_times.csv"))
)
IL_stim_firing %>% head()
Summary information of the stimulus and baseline recording files:
CELL_INFO table to store the cell categories. It was created manually using the information from the summary excel table (Glicy_juxta-fm_exp_records_injection_sum.xls)
b_d_a_MFR: Calculating the number of APs -using a custom made function (BDACalculator)- before during and after the stimulus trains (b_d_a_MFR).
b_d_a_MFR <- lapply(CELL_INFO$cell_id, BDACalculator, data = IL_stim_firing) %>%
bind_rows() %>%
mutate(FR = No_AP / train_length) %>%
dplyr::group_by(stim_cond, cell_id) %>%
summarise(MFR = mean(FR))
sd_mean_isi: Calculating the baseline MFR of the recorded IL cells from the IL_baseline_firing table using a custom made function (SDMeanISI). The results are stored in the sd_mean_isi table.
cellranks: Calculating ranks based on the activity change from “baseline” to “during stimulus”. If the activity change is negative (decreased MFR) the asigned rank is negative, if it is positive (increased MFR) the assigned rank is positive.
Calculating the firing rate change during stimulus (photoactivation of the glycinergic fibers) compared to baseline:
\[\mathbf{activity\_change} = \frac{during\_MFR - base\_MFR}{base\_MFR} * 100\]
cellranks <- b_d_a_MFR %>%
group_by(stim_cond) %>%
mutate(base_MFR = sd_mean_isi$MFR) %>%
mutate(activity_change = ((MFR-base_MFR)/base_MFR*100) %>% round(2)) %>%
dplyr::filter(stim_cond == "d") %>%
mutate(change_rank = ifelse(activity_change>0,
rank(activity_change),
-rank(-activity_change)) ) %>%
ungroup() %>%
left_join(CELL_INFO %>%
select(cell_id, control, pinch, position),
by = "cell_id")
cellranks
cellranks_before_stim: Calculating ranks based on the activity change from “before stimulus” to “during stimulus”. If the activity change is negative (decreased MFR) the asigned rank is negative, if it is positive (increased MFR) the assigned rank is positive.
Calculating the firing rate change during stimulus (photoactivation of the glycinergic fibers) compared to before stimulus:
\[\mathbf{activity\_change} = \frac{during\_MFR - before\_MFR}{before\_MFR} * 100\]
cellranks_before_stim <- b_d_a_MFR %>%
spread(key = stim_cond,value = MFR) %>%
mutate(activity_change = ((d - b)/b*100) %>% round(2)) %>%
mutate(change_rank = ifelse(activity_change > 0,
rank(activity_change),
-rank(-activity_change))
) %>%
left_join(CELL_INFO %>%
select(cell_id, control, pinch, position),
by = "cell_id")
cellranks_before_stim
TO_PLOT: Combining b_d_a_MFR (firing rate of 29 IL neurons b/d/a stim) with sd_mean_isi table (baseline firing rate of the same 29 neurons), joining with CELL_INFO containing important information of the cells (baseline activity, identified, pinched, control) and with cellranks containing the ranks asigned to each cells based on the changes in MFR during the stimulus compared to baseline.
TO_PLOT <- bind_rows(
sd_mean_isi %>%
select(MFR, cell_id, stim_cond),
b_d_a_MFR
) %>% left_join(CELL_INFO %>%
select(-file_name),
by = "cell_id") %>%
left_join(cellranks %>%
select(cell_id, change_rank, activity_change),
by = "cell_id")
datatable(TO_PLOT,
caption = "TO_PLOT table",
rownames = TRUE,
options = list(pageLength = 50, scrollX=T, scrollY="500px",dom = 't'))
Comparison of baseline and “before” stimulus firing rates in the case of spontaneously active and sponteneously inactive (pinch) neurons. Spontaneously inactive neurons showed significantly higher MFR before stiulus compared to baseline.
Firing rate change during stimulus (photoactivation of the glycinergic fibers) compared to baseline:
Firing rate change during stimulus (photoactivation of the glycinergic fibers) compared to before stimulus:
Plotting the change in MFR from “baseline” to “during stimulus”. Coloring based on the strength of the inhibition (rank)